{"action":"created","comment":{"url":"https://api.github.com/repos/choderalab/yank/pulls/comments/132284690","pull_request_review_id":55348436,"id":132284690,"diff_hunk":"@@ -10,25 +10,143 @@ the final free energy output that you get. In theory, we could just print out\n \"Free energy of Binding =  XX.XXX +- Y.YYY kcal/mol,\" but that alone does not tell you anything about the quality of\n your free energy estimate. We try to provide guides and built-in analysis to help understand the numbers YANK provides.\n \n-The analysis framework comes with a full feature API, command line auto-execution, and\n-`Jupyter Notebooks <http://jupyter.org/>`_ to help the user analyze their data programmatically, automatically, or\n-visually, depending on their choice.\n+The analysis framework comes three ways to help the user analyze their data (use these links to **jump to usage**):\n \n-**************\n-Analyzing data\n-**************\n+* :ref:`Command line auto-execution <auto_analyze>`\n+* :ref:`Cisually with Jupyter Notebooks<visual_analyze>`\n+* :ref:`Full feature API <programmatic_analyze>`","path":"docs/analysis.rst","position":14,"original_position":14,"commit_id":"e3aae585f660647a09efb47a6d8dc2f5fb202fad","original_commit_id":"e3aae585f660647a09efb47a6d8dc2f5fb202fad","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars1.githubusercontent.com/u/3656088?v=4","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"body":"Maybe just \"Programmatic Python API\"?","created_at":"2017-08-09T19:38:19Z","updated_at":"2017-08-09T19:45:04Z","html_url":"https://github.com/choderalab/yank/pull/744#discussion_r132284690","pull_request_url":"https://api.github.com/repos/choderalab/yank/pulls/744","_links":{"self":{"href":"https://api.github.com/repos/choderalab/yank/pulls/comments/132284690"},"html":{"href":"https://github.com/choderalab/yank/pull/744#discussion_r132284690"},"pull_request":{"href":"https://api.github.com/repos/choderalab/yank/pulls/744"}}},"pull_request":{"url":"https://api.github.com/repos/choderalab/yank/pulls/744","id":134970861,"html_url":"https://github.com/choderalab/yank/pull/744","diff_url":"https://github.com/choderalab/yank/pull/744.diff","patch_url":"https://github.com/choderalab/yank/pull/744.patch","issue_url":"https://api.github.com/repos/choderalab/yank/issues/744","number":744,"state":"open","locked":false,"title":"Full Site Update","user":{"login":"Lnaden","id":3809383,"avatar_url":"https://avatars1.githubusercontent.com/u/3809383?v=4","gravatar_id":"","url":"https://api.github.com/users/Lnaden","html_url":"https://github.com/Lnaden","followers_url":"https://api.github.com/users/Lnaden/followers","following_url":"https://api.github.com/users/Lnaden/following{/other_user}","gists_url":"https://api.github.com/users/Lnaden/gists{/gist_id}","starred_url":"https://api.github.com/users/Lnaden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Lnaden/subscriptions","organizations_url":"https://api.github.com/users/Lnaden/orgs","repos_url":"https://api.github.com/users/Lnaden/repos","events_url":"https://api.github.com/users/Lnaden/events{/privacy}","received_events_url":"https://api.github.com/users/Lnaden/received_events","type":"User","site_admin":false},"body":"This PR is the concluding part to the main site-updates. In this PR:\r\n\r\n* All pages now have full content\r\n* All hyperlinks tested to work\r\n* Many website typos fixed\r\n* All placeholder content filled in\r\n* Updated the Jupyter Notebook Example to reflect the current state\r\n\r\nFixes #695, Fixes #150","created_at":"2017-08-09T19:26:00Z","updated_at":"2017-08-09T19:45:05Z","closed_at":null,"merged_at":null,"merge_commit_sha":"3167aec20ff07b493e760cfca9aafd0caabd3324","assignee":null,"assignees":[],"requested_reviewers":[],"milestone":null,"commits_url":"https://api.github.com/repos/choderalab/yank/pulls/744/commits","review_comments_url":"https://api.github.com/repos/choderalab/yank/pulls/744/comments","review_comment_url":"https://api.github.com/repos/choderalab/yank/pulls/comments{/number}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/744/comments","statuses_url":"https://api.github.com/repos/choderalab/yank/statuses/e3aae585f660647a09efb47a6d8dc2f5fb202fad","head":{"label":"choderalab:update-site","ref":"update-site","sha":"e3aae585f660647a09efb47a6d8dc2f5fb202fad","user":{"login":"choderalab","id":4217481,"avatar_url":"https://avatars0.githubusercontent.com/u/4217481?v=4","gravatar_id":"","url":"https://api.github.com/users/choderalab","html_url":"https://github.com/choderalab","followers_url":"https://api.github.com/users/choderalab/followers","following_url":"https://api.github.com/users/choderalab/following{/other_user}","gists_url":"https://api.github.com/users/choderalab/gists{/gist_id}","starred_url":"https://api.github.com/users/choderalab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choderalab/subscriptions","organizations_url":"https://api.github.com/users/choderalab/orgs","repos_url":"https://api.github.com/users/choderalab/repos","events_url":"https://api.github.com/users/choderalab/events{/privacy}","received_events_url":"https://api.github.com/users/choderalab/received_events","type":"Organization","site_admin":false},"repo":{"id":13779937,"name":"yank","full_name":"choderalab/yank","owner":{"login":"choderalab","id":4217481,"avatar_url":"https://avatars0.githubusercontent.com/u/4217481?v=4","gravatar_id":"","url":"https://api.github.com/users/choderalab","html_url":"https://github.com/choderalab","followers_url":"https://api.github.com/users/choderalab/followers","following_url":"https://api.github.com/users/choderalab/following{/other_user}","gists_url":"https://api.github.com/users/choderalab/gists{/gist_id}","starred_url":"https://api.github.com/users/choderalab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choderalab/subscriptions","organizations_url":"https://api.github.com/users/choderalab/orgs","repos_url":"https://api.github.com/users/choderalab/repos","events_url":"https://api.github.com/users/choderalab/events{/privacy}","received_events_url":"https://api.github.com/users/choderalab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/choderalab/yank","description":"An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.","fork":false,"url":"https://api.github.com/repos/choderalab/yank","forks_url":"https://api.github.com/repos/choderalab/yank/forks","keys_url":"https://api.github.com/repos/choderalab/yank/keys{/key_id}","collaborators_url":"https://api.github.com/repos/choderalab/yank/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/choderalab/yank/teams","hooks_url":"https://api.github.com/repos/choderalab/yank/hooks","issue_events_url":"https://api.github.com/repos/choderalab/yank/issues/events{/number}","events_url":"https://api.github.com/repos/choderalab/yank/events","assignees_url":"https://api.github.com/repos/choderalab/yank/assignees{/user}","branches_url":"https://api.github.com/repos/choderalab/yank/branches{/branch}","tags_url":"https://api.github.com/repos/choderalab/yank/tags","blobs_url":"https://api.github.com/repos/choderalab/yank/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/choderalab/yank/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/choderalab/yank/git/refs{/sha}","trees_url":"https://api.github.com/repos/choderalab/yank/git/trees{/sha}","statuses_url":"https://api.github.com/repos/choderalab/yank/statuses/{sha}","languages_url":"https://api.github.com/repos/choderalab/yank/languages","stargazers_url":"https://api.github.com/repos/choderalab/yank/stargazers","contributors_url":"https://api.github.com/repos/choderalab/yank/contributors","subscribers_url":"https://api.github.com/repos/choderalab/yank/subscribers","subscription_url":"https://api.github.com/repos/choderalab/yank/subscription","commits_url":"https://api.github.com/repos/choderalab/yank/commits{/sha}","git_commits_url":"https://api.github.com/repos/choderalab/yank/git/commits{/sha}","comments_url":"https://api.github.com/repos/choderalab/yank/comments{/number}","issue_comment_url":"https://api.github.com/repos/choderalab/yank/issues/comments{/number}","contents_url":"https://api.github.com/repos/choderalab/yank/contents/{+path}","compare_url":"https://api.github.com/repos/choderalab/yank/compare/{base}...{head}","merges_url":"https://api.github.com/repos/choderalab/yank/merges","archive_url":"https://api.github.com/repos/choderalab/yank/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/choderalab/yank/downloads","issues_url":"https://api.github.com/repos/choderalab/yank/issues{/number}","pulls_url":"https://api.github.com/repos/choderalab/yank/pulls{/number}","milestones_url":"https://api.github.com/repos/choderalab/yank/milestones{/number}","notifications_url":"https://api.github.com/repos/choderalab/yank/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/choderalab/yank/labels{/name}","releases_url":"https://api.github.com/repos/choderalab/yank/releases{/id}","deployments_url":"https://api.github.com/repos/choderalab/yank/deployments","created_at":"2013-10-22T17:01:36Z","updated_at":"2017-05-23T00:59:42Z","pushed_at":"2017-08-09T19:26:01Z","git_url":"git://github.com/choderalab/yank.git","ssh_url":"git@github.com:choderalab/yank.git","clone_url":"https://github.com/choderalab/yank.git","svn_url":"https://github.com/choderalab/yank","homepage":"http://getyank.org","size":43090,"stargazers_count":24,"watchers_count":24,"language":"Jupyter Notebook","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":22,"mirror_url":null,"open_issues_count":108,"forks":22,"open_issues":108,"watchers":24,"default_branch":"master"}},"base":{"label":"choderalab:master","ref":"master","sha":"303feec2acf890a08efd2bd7dc73417b34fe0709","user":{"login":"choderalab","id":4217481,"avatar_url":"https://avatars0.githubusercontent.com/u/4217481?v=4","gravatar_id":"","url":"https://api.github.com/users/choderalab","html_url":"https://github.com/choderalab","followers_url":"https://api.github.com/users/choderalab/followers","following_url":"https://api.github.com/users/choderalab/following{/other_user}","gists_url":"https://api.github.com/users/choderalab/gists{/gist_id}","starred_url":"https://api.github.com/users/choderalab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choderalab/subscriptions","organizations_url":"https://api.github.com/users/choderalab/orgs","repos_url":"https://api.github.com/users/choderalab/repos","events_url":"https://api.github.com/users/choderalab/events{/privacy}","received_events_url":"https://api.github.com/users/choderalab/received_events","type":"Organization","site_admin":false},"repo":{"id":13779937,"name":"yank","full_name":"choderalab/yank","owner":{"login":"choderalab","id":4217481,"avatar_url":"https://avatars0.githubusercontent.com/u/4217481?v=4","gravatar_id":"","url":"https://api.github.com/users/choderalab","html_url":"https://github.com/choderalab","followers_url":"https://api.github.com/users/choderalab/followers","following_url":"https://api.github.com/users/choderalab/following{/other_user}","gists_url":"https://api.github.com/users/choderalab/gists{/gist_id}","starred_url":"https://api.github.com/users/choderalab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/choderalab/subscriptions","organizations_url":"https://api.github.com/users/choderalab/orgs","repos_url":"https://api.github.com/users/choderalab/repos","events_url":"https://api.github.com/users/choderalab/events{/privacy}","received_events_url":"https://api.github.com/users/choderalab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/choderalab/yank","description":"An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.","fork":false,"url":"https://api.github.com/repos/choderalab/yank","forks_url":"https://api.github.com/repos/choderalab/yank/forks","keys_url":"https://api.github.com/repos/choderalab/yank/keys{/key_id}","collaborators_url":"https://api.github.com/repos/choderalab/yank/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/choderalab/yank/teams","hooks_url":"https://api.github.com/repos/choderalab/yank/hooks","issue_events_url":"https://api.github.com/repos/choderalab/yank/issues/events{/number}","events_url":"https://api.github.com/repos/choderalab/yank/events","assignees_url":"https://api.github.com/repos/choderalab/yank/assignees{/user}","branches_url":"https://api.github.com/repos/choderalab/yank/branches{/branch}","tags_url":"https://api.github.com/repos/choderalab/yank/tags","blobs_url":"https://api.github.com/repos/choderalab/yank/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/choderalab/yank/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/choderalab/yank/git/refs{/sha}","trees_url":"https://api.github.com/repos/choderalab/yank/git/trees{/sha}","statuses_url":"https://api.github.com/repos/choderalab/yank/statuses/{sha}","languages_url":"https://api.github.com/repos/choderalab/yank/languages","stargazers_url":"https://api.github.com/repos/choderalab/yank/stargazers","contributors_url":"https://api.github.com/repos/choderalab/yank/contributors","subscribers_url":"https://api.github.com/repos/choderalab/yank/subscribers","subscription_url":"https://api.github.com/repos/choderalab/yank/subscription","commits_url":"https://api.github.com/repos/choderalab/yank/commits{/sha}","git_commits_url":"https://api.github.com/repos/choderalab/yank/git/commits{/sha}","comments_url":"https://api.github.com/repos/choderalab/yank/comments{/number}","issue_comment_url":"https://api.github.com/repos/choderalab/yank/issues/comments{/number}","contents_url":"https://api.github.com/repos/choderalab/yank/contents/{+path}","compare_url":"https://api.github.com/repos/choderalab/yank/compare/{base}...{head}","merges_url":"https://api.github.com/repos/choderalab/yank/merges","archive_url":"https://api.github.com/repos/choderalab/yank/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/choderalab/yank/downloads","issues_url":"https://api.github.com/repos/choderalab/yank/issues{/number}","pulls_url":"https://api.github.com/repos/choderalab/yank/pulls{/number}","milestones_url":"https://api.github.com/repos/choderalab/yank/milestones{/number}","notifications_url":"https://api.github.com/repos/choderalab/yank/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/choderalab/yank/labels{/name}","releases_url":"https://api.github.com/repos/choderalab/yank/releases{/id}","deployments_url":"https://api.github.com/repos/choderalab/yank/deployments","created_at":"2013-10-22T17:01:36Z","updated_at":"2017-05-23T00:59:42Z","pushed_at":"2017-08-09T19:26:01Z","git_url":"git://github.com/choderalab/yank.git","ssh_url":"git@github.com:choderalab/yank.git","clone_url":"https://github.com/choderalab/yank.git","svn_url":"https://github.com/choderalab/yank","homepage":"http://getyank.org","size":43090,"stargazers_count":24,"watchers_count":24,"language":"Jupyter Notebook","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":22,"mirror_url":null,"open_issues_count":108,"forks":22,"open_issues":108,"watchers":24,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/choderalab/yank/pulls/744"},"html":{"href":"https://github.com/choderalab/yank/pull/744"},"issue":{"href":"https://api.github.com/repos/choderalab/yank/issues/744"},"comments":{"href":"https://api.github.com/repos/choderalab/yank/issues/744/comments"},"review_comments":{"href":"https://api.github.com/repos/choderalab/yank/pulls/744/comments"},"review_comment":{"href":"https://api.github.com/repos/choderalab/yank/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/choderalab/yank/pulls/744/commits"},"statuses":{"href":"https://api.github.com/repos/choderalab/yank/statuses/e3aae585f660647a09efb47a6d8dc2f5fb202fad"}}}}
{"actor":{"display_login":"jchodera"}}